US Meat Animal Research Center Research Articles

Predicting breed composition using breed frequencies of 50,000 markers from the US Meat Animal Research Center 2,000 Bull Project1,2

Knowledge of breed composition can be useful in multiple aspects of cattle production, and can be critical for analyzing the results of whole genome-wide association studies currently being conducted around the world. We examine the feasibility and accuracy of using genotype data from the most prevalent bovine genome-wide association studies platform, the Illumina BovineSNP50 array (Illumina Inc., San Diego, CA), to estimate breed composition for individual breeds of cattle. First, allele frequencies (of Illumina-defined allele B) of SNP on the array for each of 16 beef cattle breeds were defined by genotyping a large set of more than 2,000 bulls selected in cooperation with the respective breed associations to be representative of their breed. With these breed-specific allele frequencies, the breed compositions of approximately 2,000 two-, three-, and four-way cross (of 8 breeds) cattle produced at the US Meat Animal Research Center were predicted by using a simple multiple regression technique or Mendel (http://www.genetics.ucla.edu/software/mendel) and their genotypes from the Illumina BovineSNP50 array, and were then compared with pedigree-based estimates of breed composition. The accuracy of marker-based breed composition estimates was 89% when using either estimation method for all breeds except Angus and Red Angus (averaged 79%), based on comparing estimates with pedigree-based average breed composition. Accuracy increased to approximately 88% when these 2 breeds were combined into an aggregate Angus group. Additionally, we used a subset of these markers, approximately 3,000 that populate the Illumina Bovine3K (Illumina Inc.), to see whether breed composition could be estimated with similar accuracy when using this reduced panel of SNP makers. When breed composition was estimated using only SNP in common with the Bovine 3K array, accuracy was slightly reduced to 83%. These results suggest that SNP data from these arrays could be used to estimate breed composition in most US beef cattle in situations where pedigree is not known (e.g., multiple-sire natural service matings, non-source-verified animals in feedlots or at slaughter). This approach can aid analyses that depend on knowledge of breed composition, including identification and adjustment of breed-based population stratification, when performing genome-wide association studies on populations with incomplete pedigrees. In addition, SNP-based breed composition estimates may facilitate fitting cow germplasm to the environment, managing cattle in the feedlot, and tracing disease cases back to the geographic region or farm of origin.

Prediction of genetic values for feed intake from individual body weight gain and total feed intake of the pen

Records of individual feed intake (FI) and BW gain (GN) were obtained from the Germ Plasm Evaluation (GPE) program at US Meat Animal Research Center (USMARC). Animals were randomly assigned to pens. Only pens with 6 to 9 steers (n = 289) were used for this study (data set 1). Variance components and genetic parameters were estimated using data set 1. Estimated genetic values (EGV) for FI were calculated by 5 methods using single and 2-trait analyses: 1) individual FI and individual GN, 2) individual FI alone, 3) 2-trait with individual GN but with FI missing, 4) individual GN and pen total FI, and 5) pen total FI alone. Analyses were repeated but with some of the same records assigned artificially to 36 pens of 5 and 4 paternal half sibs per pen (data sets 2 and 3). Models included year as a fixed factor and birth and weaning weights, age on test, and days fed as covariates. Estimates of heritability were 0.42 +/- 0.16 and 0.34 +/- 0.17 for FI and GN. The estimate of the genetic correlation was 0.57 +/- 0.23. Empirical responses to selection were calculated as the average EGV for the top and bottom 10% based on rank for each method but with EGV from method 1 substituted for the EGV on which ranking was based. With data set 1, rank correlations between EGV from method 1 and EGV from methods 2, 3, 4, and 5 were 0.99, 0.53, 0.32, and 0.15, respectively. Empirical responses relative to method 1 agreed with the rank correlations. Accuracy of EGV for method 4 (0.44) was greater than for method 3 (0.35) and for method 5 (0.29). Accuracies for methods 4 and 5 were greater than indicated by empirical responses and correlations with EGV from method 1. Comparisons of the 5 methods were similar for data sets 2 and 3. With data set 2, rank correlations between EGV from method 1 and EGV from methods 3, 4, and 5 were 0.47, 0.64, and 0.62. Average accuracies of 56, 75, and 75% relative to method 1 (0.67) generally agreed with the empirical responses to selection. As expected, accuracy using pen total FI and GN to obtain EGV for FI was greater than using GN alone. With data set 1, empirical response to selection with method 4 was one-third of that for method 1, although average accuracy was 65% of that for method 1. With assignment of 5 paternal half sibs to artificial pens, using pen total FI and individual GN was about 81% as effective for selection as using individual FI and GN to obtain EGV for FI and was substantially more effective than use of GN alone.

Confirmation of quantitative trait loci using a low-density single nucleotide polymorphism map for twinning and ovulation rate on bovine chromosome 51,2

Traditional genetic selection in cattle for traits with low heritability, such as reproduction, has had very little success. With the addition of DNA technologies to the genetic selection toolbox for livestock, the opportunity may exist to improve reproductive efficiency more rapidly in cattle. The US Meat Animal Research Center Production Efficiency Population has 9,186 twinning and 29,571 ovulation rate records for multiple generations of animals, but a significant number of these animals do not have tissue samples available for DNA genotyping. The objectives of this study were to confirm QTL for twinning and ovulation rate previously found on BTA5 and to evaluate the ability of GenoProb to predict genotypic information in a pedigree containing 16,035 animals when using genotypes for 24 SNP from 3 data sets containing 48, 724, or 2,900 animals. Marker data for 21 microsatellites on BTA5 with 297 to 3,395 animals per marker were used in conjunction with each data set of genotyped animals. Genotypic probabilities for females were used to calculate independent variables for regressions of additive, dominance, and imprinting effects. Genotypic regressions were fitted as fixed effects in a 2-trait mixed model analysis by using multiple-trait derivative-free REML. Each SNP was analyzed individually, followed by backward selection fitting all individually significant SNP simultaneously and then removing the least significant SNP until only significant SNP were left. Five significant SNP associations were detected for twinning rate and 3 were detected for ovulation rate. Two of these SNP, 1 for each trait, were significant for imprinting. Additional modeling of paternal and maternal allelic effects confirmed the initial results of imprinting done by contrasting heterozygotes. These results are supported by comparative mapping of mouse and human imprinted genes to this region of bovine chromosome 5.

Sensors for dynamic physiological measurements

Stress research on agricultural production animals involves monitoring of bio-energetic responses to environmental challenges. Automated monitoring of physiological and behavioral responses of animals has the advantages of reducing labor, increasing the frequency of observation, and reducing bias and observer influence, but automation requires specialized instrumentation. Equipment has been developed or adapted to meet specific monitoring needs for a range of animals and facilities. This paper summarizes work related to cattle and swine stress research at the US Meat Animal Research Center, and specifically examines recording of body temperature, respiration rate, livestock safety monitoring and electronic identification. Much of this work has been reported previously and has been consolidated here to provide an overview of sensor development and application.

Increased calf production in cattle selected for twin ovulations1,2

The effects of increasing fetal numbers and their distribution between the left and right uterine horns on calf survival, calf BW at birth and weaning, gestation length, dystocia, and calf sex ratio were evaluated for single (n = 1,587), twin (n = 2,440), and triplet calves (n = 147) born to primiparous and multiparous females in the Twinner population at the US Meat Animal Research Center between 1994 and 2004. Cattle were distributed equally between the spring and fall breeding seasons. Fetal number and distribution in utero were determined by real-time ultrasonography at 40 to 70 d postbreeding. For cows and heifers combined, number of calves per parturition increased from 1.34 in 1994 to 1.56 in 2004. Gestation length was 6.8 d shorter (P < 0.01) for twins compared with singles (277.5 +/- 0.2 vs. 284.3 +/- 0.2 d) and 12.7 d shorter for triplets (271.6 +/- 0.8 d). Survival and BW of individual calves at birth decreased (P < 0.01) but total calf BW per dam increased (P < 0.01) as fetal number increased from single to triplet births. Twins resulting from bilateral twin ovulations had increased (P < 0.01) survival and BW at birth, a longer (P < 0.01) gestation length, and less (P < 0.01) dystocia than twins resulting from unilateral twin ovulations. Calf survival and BW at birth were 97.2 +/- 0.3% and 48.0 +/- 0.1 kg for singles, 92.0 +/- 0.4% and 39.0 +/- 0.2 kg for bilateral twins, 83.2 +/- 0.4% and 36.7 +/- 0.2 kg for unilateral twins, 73.8 +/- 1.4% and 30.6 +/- 0.7 kg for bilateral triplets, and 51.9 +/- 3.2% and 31.7 +/- 1.6 kg for unilateral triplets. Birth weight of single calves increased by 0.51 kg/d for each additional day of gestation length vs. 0.38 kg/d for individual twins. Calf BW at birth increased (P < 0.01) with age of dam from 2 to 4 yr. Twin and triplet births had a greater (P < 0.01) incidence of dystocia than single births. The ratio of male:female calves (0.52:0.48) at birth was not affected by type of birth. Postnatal calf survival was similar for all 3 types of birth. Total progeny BW at weaning for single, twin, and triplet births was 217.7 +/- 2.5, 328.3 +/- 3.2, and 378.4 +/- 15.0 kg, respectively (P < 0.01). Although most bovine females have the uterine capacity to gestate twin calves, decreased survival and BW of unilateral twins and of all triplets indicate that their growth and development may have been compromised by uterine crowding.

Across-breed adjustment factors for expected progeny differences for carcass traits1

Adjustment factors to allow comparison of EPD from several breed associations for birth, weaning, and yearling weights have been available for more than 10 yr. This paper describes steps to calculate adjustment factors for EPD for 4 carcass traits: marbling score, fat thickness, ribeye area, and retail product percentage. The required information is the same as for the weight traits: 1) breed of sire solutions based on measurements on progeny at the US Meat Animal Research Center (USMARC) that have sires with breed association EPD, 2) mean EPD of sires weighted by number of progeny at USMARC (USMARC progeny not included in breed association EPD), and 3) mean EPD of nonparents from breed associations (defined as animals born 2 yr prior to calculation of EPD). Records at USM-ARC are adjusted to 100% heterozygosity because the purpose of the adjustment factors is to allow prediction of performance of progeny of sires mated to other breeds of dam. A critical step is to adjust breed of sire solutions, which are based on an earlier sample of sires, to the equivalent of a sample from a more recent nonparent group using the difference between mean EPD from information sources 2) and 3). The difference is multiplied by the coefficient of regression of USMARC progeny on EPD of their sires. With weight traits, these coefficients are not greatly different from unity. With the carcass traits, 2 sets of coefficients can be used depending on whether the EPD are based on carcass or ultrasound measurements. The regression coefficients also reflect differences in conditions for USMARC progeny (all steers) and factors associated with breed association EPD. Only for marbling score and ribeye area were any estimates of the regression coefficients near unity. For other traits, the coefficients ranged from 1.65 to 2.82. The solutions for breed of sire, differences in mean EPD, and regression coefficients are then used to calculate adjustment factors for EPD of 11 breeds including the arbitrary base breed, Angus.

Association of a single nucleotide polymorphism in SPP1 with growth traits and twinning in a cattle population selected for twinning rate1,2

Continued validation of genetic markers for economically important traits is crucial to establishing marker-assisted selection as a tool in the cattle industry. The objective of the current study was to evaluate the association of a SNP (T(9)/T(10)) in the osteopontin gene (SPP1) with growth rate in a large cattle population spanning multiple generations and representing alleles from 12 founding breeds. This population has been maintained at the US Meat Animal Research Center since 1981 and subjected to selection for twinning rate. Phenotypic records for this population included twinning rate and ovulation rate, providing an opportunity to examine the potential effects of SPP1 genotype on reproductive traits. A set of 2,701 animals was geno-typed for the T(9)/T(10) polymorphism at SPP1. The geno-typic data, including previously genotyped markers on chromosome 6 (BTA6), were used in conjunction with pedigree information to estimate genotypic probabilities for all 14,714 animals with phenotypic records. The genotypic probabilities for females were used to calculate independent variables for regressions of additive, dominance, and imprinting effects. Genotypic regressions were fit as fixed effects in a mixed model analysis, in which each trait was analyzed in a 2-trait model where single births were treated as a separate trait from twin births. The association of the SPP1 marker with birth weight (P < 0.006), weaning weight (P < 0.007), and yearling weight (P < 0.003) was consistent with the previously reported effects of SPP1 genotype on yearling weight. Our data supports the conclusion that the SNP successfully tracks functional alleles affecting growth in cattle. The previously undetected effect of the SNP on birth and weaning weight suggests this particular SPP1 marker may explain a portion of the phenotypic variance explained by QTL for birth and HCW on BTA6.

Comparing Genetic Value of Bulls from Different Breeds: Across Breed EPDs

AN162, a 5-page fact sheet by Gary R. Hansen, describes how to use tables developed by the US Meat Animal Research Center (MARC) which provide adjustment factors to allow for the calculation of across-breed expected progeny differences (AB-EPDs) to assess genetic potential across different breeds. Published by the UF Department of Animal Science, March 2006.

Effects of age, weight, and fat slaughter end points on estimates of breed and retained heterosis effects for carcass traits

The influence of different levels of adjusted fat thickness (AFT) and HCW slaughter end points (covariates) on estimates of breed and retained heterosis effects was studied for 14 carcass traits from serially slaughtered purebred and composite steers from the US Meat Animal Research Center (MARC). Contrasts among breed solutions were estimated at 0.7, 1.1, and 1.5 cm of AFT, and at 295.1, 340.5, and 385.9 kg of HCW. For constant slaughter age, contrasts were adjusted to the overall mean (432.5 d). Breed effects for Red Poll, Hereford, Limousin, Braunvieh, Pinzgauer, Gelbvieh, Simmental, Charolais, MARC I, MARC II, and MARC III were estimated as deviations from Angus. In addition, purebreds were pooled into 3 groups based on lean-to-fat ratio, and then differences were estimated among groups. Retention of combined individual and maternal heterosis was estimated for each composite. Mean retained heterosis for the 3 composites also was estimated. Breed rankings and expression of heterosis varied within and among end points. For example, Charolais had greater (P < 0.05) dressing percentages than Angus at the 2 largest levels of AFT and smaller (P < 0.01) percentages at the 2 largest levels of HCW, whereas the 2 breeds did not differ (P > or = 0.05) at a constant age. The MARC III composite produced 9.7 kg more (P < 0.01) fat than Angus at AFT of 0.7 cm, but 7.9 kg less (P < 0.05) at AFT of 1.5 cm. For MARC III, the estimate of retained heterosis for HCW was significant (P < 0.05) at the lowest level of AFT, but at the intermediate and greatest levels estimates were nil. The pattern was the same for MARC I and MARC III for LM area. Adjustment for age resulted in near zero estimates of retained heterosis for AFT, and similarly, adjustment for HCW resulted in nil estimates of retained heterosis for LM area. For actual retail product as a percentage of HCW, the estimate of retained heterosis for MARC III was negative (-1.27%; P < 0.05) at 0.7 cm but was significantly positive (2.55%; P < 0.05) at 1.5 cm of AFT. Furthermore, for MARC III, estimates of heterosis for some traits (fat as a percentage of HCW as another example) also doubled in magnitude depending on different levels of AFT end point. Rational exploitation of breeds requires special attention to use of different end points and levels of those end points, mainly for fat thickness.

Genetic Relationships Between Male and Female Reproductive Traits in Beef Cattle

AbstractReproductive traits were measured for 234 bulls and 1184 heifers from matings of three dam breeds (Angus, Hereford, and MARC III) with six sire breeds (Angus, Hereford, Brahman, Boran, Tuli, and Belgian Blue) from the Germ Plasm Evaluation (GPE) Program at Roman L. Hruska US Meat Animal Research Center. Male traits were yearling scrotal circumference (YSC), height (YH), and yearling BW; age at puberty (API; production of 50 million sperm with ≥10% progressive motility); age, scrotal circumference, average testis length, and testicular volume when 500 million sperm were produced with ≥50% progressive motility (AP3, SC3, L3 and V3, respectively); and 15-mo BW (15W) and height (15H). Traits of females were age at puberty (AP, first estrus) and pregnancy rate (PR) at 18 mo. The objective was to determine whether indirect selection on male traits would be effective for improving female fertility traits. Selection of males on AP1, AP3, SC3, L3, V3, YH, 15W, and 15H may be useful for improving PR because of genetic correlations and low heritability for PR. Although no male trait was found to be effective for improving AP in females through indirect selection, YSC and SC3 were the most favorable. If heritability were as large as estimated in this study for AP (0.52), direct rather than indirect selection would seem to be more effective for AP in heifers, although the difficulty of measuring AP in heifers also would need to be considered. Male reproductive traits, such as scrotal circumference and also YH and 15H, however, are easier and less expensive to measure than female reproductive traits, and greater selection intensity can be applied to these male traits.

Linkage and RH mapping of the porcine adiponectin gene on chromosome 13

USDA ARS, US Meat AnimalResearch Center, Spur 18D, PO Box 166, Clay Center, NE 68933-0166, USAAccepted for publication 17 March 2005Source/description: A fragment of the porcine adipocyte, C1Qand collagen domain containing (ADIPOQ) gene, whichencodes adiponectin, was amplified using primer pair A(Table 1). These primers were designed based on the humancDNA sequence (GenBank accession no. NM_004797), whichwas aligned to bovine cDNA (AF269230) and human genomic(NT_004962) sequences in order to determine conservedregions and exon–intron boundaries of the gene respectively.An amplicon of approximately 1.8 kb was cloned andsequenced. The sequence was used to design porcine primerpair B (Table 1), which produced a 1417 bp amplicon. Thesequence was extended by an inverse polymerase chain reac-tion (PCR) strategy

Linkage mapping of the porcine chromogranin B (CHGB) gene to chromosome 171

Animal GeneticsVolume 36, Issue 2 p. 168-168 Linkage mapping of the porcine chromogranin B (CHGB) gene to chromosome 171 J. G. Kim, J. G. Kim US Department of Agriculture, Agricultural Research Service, and US Meat Animal Research Center, Clay Center, NE, USA. Present address: Department of Pathology, LSU Health Science Center, School of Medicine, New Orleans, LA, USASearch for more papers by this authorD. Nonneman, D. Nonneman US Department of Agriculture, Agricultural Research Service, and US Meat Animal Research Center, Clay Center, NE, USA. Present address: Department of Pathology, LSU Health Science Center, School of Medicine, New Orleans, LA, USASearch for more papers by this authorJ. L. Vallet, J. L. Vallet US Department of Agriculture, Agricultural Research Service, and US Meat Animal Research Center, Clay Center, NE, USA. Present address: Department of Pathology, LSU Health Science Center, School of Medicine, New Orleans, LA, USASearch for more papers by this authorG. A. Rohrer, G. A. Rohrer US Department of Agriculture, Agricultural Research Service, and US Meat Animal Research Center, Clay Center, NE, USA. Present address: Department of Pathology, LSU Health Science Center, School of Medicine, New Orleans, LA, USASearch for more papers by this authorR. K. Christenson, R. K. Christenson US Department of Agriculture, Agricultural Research Service, and US Meat Animal Research Center, Clay Center, NE, USA. Present address: Department of Pathology, LSU Health Science Center, School of Medicine, New Orleans, LA, USASearch for more papers by this author J. G. Kim, J. G. Kim US Department of Agriculture, Agricultural Research Service, and US Meat Animal Research Center, Clay Center, NE, USA. Present address: Department of Pathology, LSU Health Science Center, School of Medicine, New Orleans, LA, USASearch for more papers by this authorD. Nonneman, D. Nonneman US Department of Agriculture, Agricultural Research Service, and US Meat Animal Research Center, Clay Center, NE, USA. Present address: Department of Pathology, LSU Health Science Center, School of Medicine, New Orleans, LA, USASearch for more papers by this authorJ. L. Vallet, J. L. Vallet US Department of Agriculture, Agricultural Research Service, and US Meat Animal Research Center, Clay Center, NE, USA. Present address: Department of Pathology, LSU Health Science Center, School of Medicine, New Orleans, LA, USASearch for more papers by this authorG. A. Rohrer, G. A. Rohrer US Department of Agriculture, Agricultural Research Service, and US Meat Animal Research Center, Clay Center, NE, USA. Present address: Department of Pathology, LSU Health Science Center, School of Medicine, New Orleans, LA, USASearch for more papers by this authorR. K. Christenson, R. K. Christenson US Department of Agriculture, Agricultural Research Service, and US Meat Animal Research Center, Clay Center, NE, USA. Present address: Department of Pathology, LSU Health Science Center, School of Medicine, New Orleans, LA, USASearch for more papers by this author First published: 31 March 2005 https://doi.org/10.1111/j.1365-2052.2005.01241.x Ronald K. Christenson ([email protected]) 1 Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume36, Issue2April 2005Pages 168-168 RelatedInformation

Genetic relationships between sex-specific traits in beef cattle: Mature weight, weight adjusted for body condition score, height and body condition score of cows, and carcass traits of their steer relatives1

Data from the first four cycles of the Germplasm Evaluation Program at the U.S. Meat Animal Research Center (USMARC) were used to investigate genetic relationships between mature weight (MW, n = 37,710), mature weight adjusted for body condition score (AMW, n = 37,676), mature height (HT, n = 37,123), and BCS (n = 37,676) from 4- to 8-yr old cows (n = 1,800) and carcass traits (n = 4,027) measured on their crossbred paternal half-sib steers. Covariance components among traits were estimated using REML. Carcass traits were adjusted for age at slaughter. Estimates of heritability for hot carcass weight (HCWT); percentage of retail product; percentage of fat; percentage of bone; longissimus muscle area; fat thickness adjusted visually; estimated kidney, pelvic, and heart fat percentage; marbling score; Warner-Bratzler shear force; and taste panel tenderness measured on steers were moderate to high (0.26 to 0.65), suggesting that selection for carcass and meat traits could be effective. Estimates of heritability for taste panel flavor and taste panel juiciness were low and negligible (0.05 and 0.01, respectively). Estimates of heritability from cow data over all ages and seasons were high for MW, AMW, and HT (0.52, 0.57, 0.71; respectively) and relatively low for BCS (0.16). Pairwise analyses for each female mature trait with each carcass trait were done with bivariate animal models. Estimates of genetic correlations between cow mature size and carcass composition or meat quality traits, with the exception of HCWT, were relatively low. Selection for cow mature size (weight and/or height) could be effective and would not be expected to result in much, if any, correlated changes in carcass and meat composition traits. However, genetic correlations of cow traits, with the possible exception of BCS, with HCWT may be too large to ignore. Selection for steers with greater HCWT would lead to larger cows.

Genetic relationships between sex-specific traits in beef cattle: Mature weight, weight adjusted for body condition score, height and body condition score of cows, and carcass traits of their steer relatives1

Data from the first four cycles of the Germplasm Evaluation Program at the U.S. Meat Animal Research Center (USMARC) were used to investigate genetic relationships between mature weight (MW, n = 37,710), mature weight adjusted for body condition score (AMW, n = 37,676), mature height (HT, n = 37,123), and BCS (n = 37,676) from 4- to 8-yr old cows (n = 1,800) and carcass traits (n = 4,027) measured on their crossbred paternal half-sib steers. Covariance components among traits were estimated using REML. Carcass traits were adjusted for age at slaughter. Estimates of heritability for hot carcass weight (HCWT); percentage of retail product; percentage of fat; percentage of bone; longissimus muscle area; fat thickness adjusted visually; estimated kidney, pelvic, and heart fat percentage; marbling score; Warner-Bratzler shear force; and taste panel tenderness measured on steers were moderate to high (0.26 to 0.65), suggesting that selection for carcass and meat traits could be effective. Estimates of heritability for taste panel flavor and taste panel juiciness were low and negligible (0.05 and 0.01, respectively). Estimates of heritability from cow data over all ages and seasons were high for MW, AMW, and HT (0.52, 0.57, 0.71; respectively) and relatively low for BCS (0.16). Pairwise analyses for each female mature trait with each carcass trait were done with bivariate animal models. Estimates of genetic correlations between cow mature size and carcass composition or meat quality traits, with the exception of HCWT, were relatively low. Selection for cow mature size (weight and/or height) could be effective and would not be expected to result in much, if any, correlated changes in carcass and meat composition traits. However, genetic correlations of cow traits, with the possible exception of BCS, with HCWT may be too large to ignore. Selection for steers with greater HCWT would lead to larger cows.

Mapping microsatellite markers identified in porcine EST sequences.

A sequence search of swine expressed sequence tags (EST) data in GenBank identified over 100 sequence files which contained a microsatellite repeat or simple sequence repeat (SSR). Most of these repeat motifs were dinucleotide (CA/GT) repeats; however, a number of tri-, tetra-, penta- and hexa-nucleotide repeats were also detected. An initial assessment of six dinucleotide and 14 higher-order repeat markers indicated that only dinucleotide markers yielded a sufficient number of informative markers (100% vs. 14% for dinucleotide and higher order repeats, respectively). Primers were designed for an additional 50 di- and one tri-nucleotide SSRs. Overall, 42 markers were polymorphic in the US Meat Animal Research Center (MARC) reference population, 17 markers were uninformative and 12 primer pairs failed to satisfactorily amplify genomic DNA. A comparison of di-nucleotide repeat vs. markers with repeat motifs of three to six bases demonstrated that 72% of dinucleotide markers were informative relative to only 7% of other repeat motifs. The difference was the result of a much higher percentage of monomorphic markers in the three to six base repeat motif markers than in the dinucleotide markers (64% vs. 14%). Either higher order repeat motifs are less polymorphic in the porcine genome or our selection criteria for repeat length of more than 17 contiguous bases was too low. The mapped microsatellite markers add to the porcine genetic map and provide valuable links between the porcine and human genome.

DEVELOPMENT OF RUGGED ENVIRONMENTAL MONITORING UNITS FOR HUMIDITY AND TEMPERATURE

Research on the effects of thermal environments requires monitoring and control based on temperature andhumidity measurements. There are many approaches to both temperature and humidity measurements, but few offer highreliability in hostile environments with acceptable accuracy and relatively low cost. The Biological Engineering ResearchUnit at the U.S. Meat Animal Research Center (USMARC) evaluated two separate units that were developed withcommercially available sensors for meeting the cost/performance criteria: 1) a linear temperature sensor designed arounda National Semiconductor LM35CA, and 2) an Ohmic Instruments Company ABS 300 sensor. This article details sensorcalibration and performance.

Electrical conductivity monitoring of soil condition and available N with animal manure and a cover crop

Development of sustainable agricultural management systems will depend, in part, on the ability to better use renewable resources, such as animal manure, and to synchronize the levels of soil available N with crop plant needs during the growing season. This study was conducted at the US Meat Animal Research Center in the central USA to determine whether differences in electromagnetic (EM) soil conductivity and available N levels over a growing season can be linked to feedlot manure/compost application and use of a green winter cover crop. A series of soil conductivity maps of a research cornfield were generated using global positioning system (GPS) and EM induction methods. The study site was treated over a 7-year period with manure and compost at rates matching either the phosphorus or the nitrogen requirements of silage corn (Zea mays L.). The plot was split for sub-treatments of a rye (Secale cereale L.) winter cover crop and no cover crop. Image processing techniques were used to establish electrical conductivity (EC) treatment means for each of the growing season surveys. Sequential measurement of profile weighted soil electrical conductivity (ECa) was effective in identifying the dynamic changes in available soil N, as affected by animal manure and N fertilizer treatments, during the corn-growing season. This method also clearly identified the effectiveness of cover crops in minimizing levels of available soil N before and after the corn-growing season, when soluble N is most subject to loss. The EM method for assessing soil condition provides insights into the dynamics of available N transformations that are supported by soil chemical analyses. This real-time monitoring approach could also be useful to farmers in enhancing N use efficiencies of cropping management systems and in minimizing N losses to the environment.

Mapping genes located on human chromosomes 2 and 12 to porcine chromosomes 15 and 5.

Informative microsatellites associated with two genes on HSA12 (lysozyme, LYZ; tumour necrosis factor receptor, TNFR) and one gene on HSA2 (glutamic acid decarboxylase 1, GAD1) were mapped in the US Meat Animal Research Center (MARC) swine reference population and the physical assignment of a-lactalbumin (LALBA) was determined. A comparative map for HSA2 and HSA12 with SSC15 and SSC5, respectively, was developed by combining the results from this study with published type I loci mapped in both species. One rearrangement between HSA2 and SSC15 was detected while the number of rearrangements between HSA12 and SSC5 were numerous. These results indicated that conservation of synteny does not imply a conservation of gene order and that additional type I markers need to be mapped in the pig to fully understand the chromosomal rearrangements that occurred during the evolution of mammals.

A consensus linkage map for swine chromosome 7

The First International Workshop on Swine Chromosome 7 (SSC7) was held in Minnesuing, Wisconsin, USA on 21–24 September 1995. The objective was to develop a comprehensive linkage map for porcine chromosome 7 by combining genotypic data from four swine reference populations. Contributions of genotypic data were made from the US Meat Animal Research Center, the University of Minnesota, the PiGMaP consortium and the Scandinavian consortium. Primers for selected sequence tagged site markers, to be genotyped across the reference populations, were exchanged to integrate individual maps of SSC7. Eighty‐six loci were genotyped; these loci represented microsatellite, minisatellite, single‐strand conformation polymorphism, restriction fragment length polymorphism, erythrocyte antigen and protein polymorphisms. Eighteen genes were mapped, including 12 markers within class I, class II and class III regions (four markers in each class) of the swine major histocompatibility complex. Forty‐two markers were either genotyped on more than one population or were included in a haplotype system and used to develop skeletal linkage maps that spanned 147·6, 212·7 and 179·5 cM for the male, female and sex‐average maps, respectively. A comprehensive linkage map was developed incorporating those markers with more than 30 informative meioses. The comprehensive map was slightly longer than the skeletal map, at 153·3, 215·3 and 183·8 cM, respectively, with only three intervals greater than 10 cM. These results significantly improve the genetic resolution of the porcine chromosome 7 map and represent an accurate approach for the merging of genetic maps produced in different reference populations.

Rick factors for seroprevalence of ovine lentivirus in breeding ewe flocks in Nebraska, USA

The prevalence of and risk factors for ovine lentivirus (OLV) infection in 1466 breeding ewes in nine US Meat Animal Research Center (MARC) flocks were determined using a recombinant transmembrane protein (rTM) enzyme-linked immunosorbent assay (ELISA) to detect serum anti-OLV antibodies and define infection. Based on multivariable logistic regression, confinement birth and rearing (odds ratio (OR) = 1.6), older weaning ages (OR = 1.1 week −1), and older age (OR = 1.3−2.5 year −1 beyond age 1 year) were significantly associated with higher OLV prevalence in ewes. Prevalence also varied significantly by flock, with Finnsheep and Texel ewes having the highest prevalences and Booroola Merino and Suffolk ewes having the lowest prevalences. These findings support the hypothesis that management control efforts should concentrate on events early in the life of sheep, as this period is associated with factors which can modulate the risk for OLV infection.